-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 Muk0XOOJeTbabLkNtn0DYxen3PUmKTrzd3+LoU+1gbQSNJPGJyOBlkZq5YryRgbD
 YDel/csE9ADyjHZgDWFfBA==

<SEC-DOCUMENT>0001231977-06-000044.txt : 20061017
<SEC-HEADER>0001231977-06-000044.hdr.sgml : 20061017
<ACCEPTANCE-DATETIME>20061017120146
ACCESSION NUMBER:		0001231977-06-000044
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20061016
FILED AS OF DATE:		20061017
DATE AS OF CHANGE:		20061017

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ALEXION PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0000899866
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				133648318
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		352 KNOTTER DRIVE
		CITY:			CHESHIRE
		STATE:			CT
		ZIP:			06511
		BUSINESS PHONE:		2037761790

	MAIL ADDRESS:	
		STREET 1:		352 KNOTTER DRIVE
		CITY:			CHESHIRE
		STATE:			CT
		ZIP:			06511

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			BELL LEONARD
		CENTRAL INDEX KEY:			0001231949

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-27756
		FILM NUMBER:		061148019

	MAIL ADDRESS:	
		STREET 1:		C/O ALEXION PHARMACEUTICALS INC
		STREET 2:		352 KNOTTER DRIVE
		CITY:			CHESHIRE
		STATE:			CT
		ZIP:			06410
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>primary_doc.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-10-16</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000899866</issuerCik>
        <issuerName>ALEXION PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>alxn</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001231949</rptOwnerCik>
            <rptOwnerName>BELL LEONARD</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ALEXION PHARMACEUTICALS INC</rptOwnerStreet1>
            <rptOwnerStreet2>352 KNOTTER DRIVE</rptOwnerStreet2>
            <rptOwnerCity>CHESHIRE</rptOwnerCity>
            <rptOwnerState>CT</rptOwnerState>
            <rptOwnerZipCode>06410</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Executive Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.0001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2006-10-16</value>
            </transactionDate>
            <deemedExecutionDate>
                <value>2006-10-16</value>
            </deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>30000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>10.38</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>360399</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>COmmon Stock, par value #0.0001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2006-10-16</value>
            </transactionDate>
            <deemedExecutionDate>
                <value>2006-10-16</value>
            </deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>15600</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>37.85</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>344799</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.0001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2006-10-16</value>
            </transactionDate>
            <deemedExecutionDate>
                <value>2006-10-16</value>
            </deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>4500</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>37.87</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>340299</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Option to purchase Common Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>10.38</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-10-16</value>
            </transactionDate>
            <deemedExecutionDate>
                <value>2008-10-16</value>
            </deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>30000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2001-04-01</value>
            </exerciseDate>
            <expirationDate>
                <value>2007-04-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, par value $0.0001 per share</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>30000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>90000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <ownerSignature>
        <signatureName>Leonard Bell</signatureName>
        <signatureDate>2006-10-17</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----